First, relax and take a deep breath. BCG is an attenuated modified bacterium that was initially developed in the 1920's to inoculate children against TB.
It will not cause TB in anyone. It is extremely unlikely that you or anyone in your family are at any risk, unless, for example, they had an immune deficiency disease. The precautions are there for basic hygiene.

Yes, even if you are on a septic system, I would not imagine that a few pieces of toilet paper would screw it up, so I would suggest she flush it for the six hours.
After that time all BCG should be pretty well out of her system. I used a maxi-pad for the afternoon after BCG administration, and wrapped it carefully before I threw it away.

BCG can cause problems, for example, if a patient had an open wound in the bladder at the time of instillation. That is why the urologist always checks for a UTI or blood in the urine first, and often postpones a treatment if any problems exist. But this would be a case of the bacteria getting into the patient's blood stream.

Thousands of us have had BCG treatments and I know of no one whose family has had any problems. Your mom should just follow her doctor's instructions and follow basic rules...ie, wash her hands carefully.

You will all be just fine. Your mom can use your support, as she may feel crampy and fatigued after her treatment, for up to a day or so.

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